I've never (thankfully) played the CDi titles, so I can't comment.

A Link to The Past
Link's Awakening
Four Swords Adventure

What was your least favorite part?

Was it the empty overworld?

Or was it having to mill about the castle town talking to uninteresting people rather than doing something that felt like a Zelda game?

Or was it the mediocre camera control?

 

All of that, the auto-jumping, Navi never shutting up, mostly just the overall feel of the game. I've gone back a few times and tried to play it again(I even have the improved GC collection version) and I can't even make it out of the fairy village without just turning it off. Biggest disappointment of the N64 era for me. We had it preordered for ages, got the snazzy gold cartridge and everything. 
 

wel it looks like you found somethin to bitch about anyway!  

lol that was the point.

Ocarina for console, easily, although BOTW certainly has potential to be up there. Still too early to say.

Link's Awakening for handheld, but I also really love Oracle of Seasons. I played LA again a couple months ago so it's fresh in my mind, I haven't play OOS since it came out so I'm not sure how it has aged.

I accidentally voted for Four Swords but I meant to vote Tri Force Heroes. Playing that with two of my buddies was one of the more fun multiplayer experiences I've had with any game.

And I've never played any of the CD-I titles so I didn't vote on that.